NOT NULL constraint failed: genes.gene_id

[dawn1313]

Hi,

I am using readCufflinks but got the following error:

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> cuff_data <- readCufflinks('EFt_bwa',gtfFile="transcripts.gtf",genome="gi|157779983|gb|EF999921.1|",rebuild=T)
Creating database EFt_bwa/cuffData.db
Reading Run Info File EFt_bwa/run.info
Writing runInfo Table
Reading Read Group Info EFt_bwa/read_groups.info
Writing replicates Table
Reading Var Model Info EFt_bwa/var_model.info
Writing varModel Table
Reading GTF file
Writing GTF features to 'features' table...
Reading EFt_bwa/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Error in sqliteSendQuery(con, statement, bind.data) :
rsqlite_query_send: could not execute: NOT NULL constraint failed: genes.gene_id
-----------------------

The file transcripts.gtf (see below) was generated by Cufflinks "cufflinks -p 8 -G /rsgrps/fgoodrum/Referance/ref_annotation.gff3 ../cleant6_bwa_sortedc.bam" , where the bam file was from the POOLED total reads file mapping to the reference, and transcripts.gtf was used for cuffdiff.
-------------------------------
[Victoria@service0 cuffdiff]$ head -3 transcripts.gtf

gi|157779983|gb|EF999921.1| Cufflinks transcript 331 1008 1000 - . gene_id ""; transcript_id "US7"; FPKM "230.5778142799"; frac "1.000000"; conf_lo "216.465711"; conf_hi "244.689918"; cov "554.839664";

gi|157779983|gb|EF999921.1| Cufflinks exon 331 1008 1000 - . gene_id ""; transcript_id "US7"; exon_number "1"; FPKM "230.5778142799"; frac "1.000000"; conf_lo "216.465711"; conf_hi "244.689918"; cov "554.839664";

gi|157779983|gb|EF999921.1| Cufflinks transcript 1210 1890 1000 - . gene_id ""; transcript_id "US8"; FPKM "1792.6752448517"; frac "1.000000"; conf_lo "1752.861299"; conf_hi "1832.489191"; cov "4365.956341";
--------------------

For the cuffdiff results, it seems only isoform_exp.diff has records but no records for others (genes, cds etc).

Thank you!
Victoria